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epi2me-labs / wf-amplicon

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Process `pipeline:deNovoPipeline_spoa:spoa (1)` terminated with an error exit status (1) #19

Closed Andreas-Bio closed 3 months ago

Andreas-Bio commented 4 months ago

Operating System

Windows 10

Other Linux

No response

Workflow Version

wf-amplicon v1.1.0

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

The error message is too cryptic. I dont know where to start with the debugging. "Process pipeline:deNovoPipeline_spoa:spoa (1) terminated with an error exit status (1)" report.html.txt

Can you please provide me with some ideas where to start?

Relevant log output

Jul-06 06:46:24.912 [main] DEBUG nextflow.cli.Launcher - $> /mnt/c/Users/Pete/AppData/Local/EPI2ME/app-5.1.14/resources/nextflow-all -log /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/nextflow.log run /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/main.nf -params-file /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/params.json -w /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work -ansi-log false -offline -profile standard -with-weblog 'http://172.25.192.1:52436' -name zealous_heyrovsky -c /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/local.config
Jul-06 06:46:24.952 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.2
Jul-06 06:46:24.983 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/mnt/c/Users/Pete/epi2melabs/workflows/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3
Jul-06 06:46:25.000 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-06 06:46:25.003 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-06 06:46:25.007 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jul-06 06:46:25.023 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jul-06 06:46:25.039 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/nextflow.config
Jul-06 06:46:25.043 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/local.config
Jul-06 06:46:25.043 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/nextflow.config
Jul-06 06:46:25.044 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/local.config
Jul-06 06:46:25.085 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jul-06 06:46:25.834 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jul-06 06:46:25.882 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jul-06 06:46:25.893 [main] INFO  nextflow.cli.CmdRun - Launching `/mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/main.nf` [zealous_heyrovsky] DSL2 - revision: e995d87ced
Jul-06 06:46:25.893 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-06 06:46:25.894 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-06 06:46:25.915 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /mnt/c/Users/Pete/epi2melabs/workflows/.nextflow/secrets/store.json
Jul-06 06:46:25.920 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@208205ed] - activable => nextflow.secret.LocalSecretsProvider@208205ed
Jul-06 06:46:25.992 [main] DEBUG nextflow.Session - Session UUID: a5d4b858-8252-443c-b064-9dfc9ed671f7
Jul-06 06:46:25.992 [main] DEBUG nextflow.Session - Run name: zealous_heyrovsky
Jul-06 06:46:25.993 [main] DEBUG nextflow.Session - Executor pool size: 24
Jul-06 06:46:26.004 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=72; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-06 06:46:26.025 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.2 build 5871
  Created: 08-06-2023 09:33 UTC (09:33 GMT)
  System: Linux 5.15.153.1-microsoft-standard-WSL2
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.21+9-post-Ubuntu-0ubuntu122.04
  Encoding: UTF-8 (UTF-8)
  Process: 8023@ATB [127.0.1.1]
  CPUs: 24 - Mem: 31.3 GB (20.5 GB) - Swap: 8 GB (8 GB)
Jul-06 06:46:26.058 [main] DEBUG nextflow.Session - Work-dir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work [v9fs]
Jul-06 06:46:26.107 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[GoogleLifeSciencesExecutor, AwsBatchExecutor, GoogleBatchExecutor]
Jul-06 06:46:26.120 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-06 06:46:26.150 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jul-06 06:46:26.167 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jul-06 06:46:26.201 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-06 06:46:26.311 [main] DEBUG nextflow.Session - Session start
Jul-06 06:46:26.315 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/output/execution/trace.txt
Jul-06 06:46:26.330 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/lib
Jul-06 06:46:26.356 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/lib
Jul-06 06:46:26.358 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/lib/nfcore_external_java_deps.jar
Jul-06 06:46:26.416 [Actor Thread 2] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:27.956 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-06 06:46:29.920 [main] INFO  nextflow.Nextflow - 
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-amplicon v1.1.0
--------------------------------------------------------------------------------
Core Nextflow options
  runName                    : zealous_heyrovsky
  containerEngine            : docker
  launchDir                  : /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9
  workDir                    : /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work
  projectDir                 : /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon
  userName                   : epi2mewsl
  profile                    : standard
  configFiles                : /mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/nextflow.config, /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/local.config

Input Options
  fastq                      : /mnt/e/ONT/RUN18_beeITS2_refDat/test

De-novo Consensus Options
  force_spoa_length_threshold: 1000

Output Options
  out_dir                    : /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/output

Miscellaneous Options
  threads                    : 6

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-amplicon for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-amplicon v1.1.0.
--------------------------------------------------------------------------------
Jul-06 06:46:30.603 [main] INFO  nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Jul-06 06:46:30.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name fastcat
Jul-06 06:46:30.784 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.785 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.789 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-06 06:46:30.796 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=22; memory=45 GB; capacity=24; pollInterval=100ms; dumpInterval=5m
Jul-06 06:46:30.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:getVersions
Jul-06 06:46:30.870 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.871 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.873 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name pipeline:addMedakaToVersionsFile
Jul-06 06:46:30.873 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.873 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:getParams
Jul-06 06:46:30.876 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.876 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.886 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:subsetReads
Jul-06 06:46:30.887 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.887 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.894 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:porechop
Jul-06 06:46:30.895 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.895 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.929 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:lookupMedakaModel
Jul-06 06:46:30.930 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.930 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.937 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:miniasm
Jul-06 06:46:30.938 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.938 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.944 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:racon
Jul-06 06:46:30.945 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.945 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:alignDraft
Jul-06 06:46:30.948 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.949 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.953 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name pipeline:deNovoPipeline_asm:medakaConsensus
Jul-06 06:46:30.953 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.953 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.956 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:bamstatsDraft
Jul-06 06:46:30.957 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.957 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.959 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:mosdepthPerBase
Jul-06 06:46:30.960 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.960 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.966 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:trimAndQC
Jul-06 06:46:30.966 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.967 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.971 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:alignPolished
Jul-06 06:46:30.972 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.972 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.974 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:bamstatsPolished
Jul-06 06:46:30.975 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.975 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:30.979 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_asm:mosdepthWindows
Jul-06 06:46:30.980 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:30.980 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.010 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:lookupMedakaModel
Jul-06 06:46:31.010 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.011 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name pipeline:deNovoPipeline_spoa:spoa
Jul-06 06:46:31.014 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.014 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.016 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:alignDraft
Jul-06 06:46:31.016 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.016 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.019 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:medaka` matches labels `medaka` for process with name pipeline:deNovoPipeline_spoa:medakaConsensus
Jul-06 06:46:31.019 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.019 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.021 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:bamstatsDraft
Jul-06 06:46:31.021 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.021 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:mosdepthPerBase
Jul-06 06:46:31.023 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.023 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.025 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:trimAndQC
Jul-06 06:46:31.026 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.026 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.028 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:alignPolished
Jul-06 06:46:31.029 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.029 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.030 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:bamstatsPolished
Jul-06 06:46:31.030 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.030 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.031 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:deNovoPipeline_spoa:mosdepthWindows
Jul-06 06:46:31.032 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.032 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.044 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:concatTSVs
Jul-06 06:46:31.044 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.044 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.047 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:catFastqIntoFasta
Jul-06 06:46:31.047 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.047 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.054 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:collectFilesInDir
Jul-06 06:46:31.054 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.054 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.056 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name pipeline:makeReport
Jul-06 06:46:31.056 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.056 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.079 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `wf_common` for process with name pipeline:configure_igv
Jul-06 06:46:31.080 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.080 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.091 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wfamplicon` matches labels `wfamplicon` for process with name output
Jul-06 06:46:31.091 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-06 06:46:31.091 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-06 06:46:31.092 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: move_or_compress_fq_file, pipeline:getParams, pipeline:deNovoPipeline_spoa:mosdepthWindows, mosdepthWindows, pipeline:deNovoPipeline_spoa:mosdepthPerBase, racon, pipeline:deNovoPipeline_spoa:bamstatsDraft, bamstatsPolished, pipeline:addMedakaToVersionsFile, mergeBAMs, checkBamHeaders, alignReads, mergeBams, output, pipeline:deNovoPipeline_asm:trimAndQC, medakaVariant, makeReport, getVersions, pipeline:deNovoPipeline_spoa:lookupMedakaModel, validateIndex, pipeline:deNovoPipeline_asm:bamstatsDraft, pipeline:deNovoPipeline_asm:miniasm, pipeline:deNovoPipeline_asm:lookupMedakaModel, pipeline:deNovoPipeline_spoa:alignDraft, pipeline:catFastqIntoFasta, bamstats, pipeline:deNovoPipeline_spoa:bamstatsPolished, pipeline:subsetReads, downsampleReads, pipeline:deNovoPipeline_spoa:trimAndQC, downsampleBAMforMedaka, fastcat, miniasm, pipeline:deNovoPipeline_asm:mosdepthWindows, lookupMedakaModel, subsetReads, pipeline:configure_igv, collectFilesInDir, mosdepthPerBase, samtools_index, getParams, pipeline:deNovoPipeline_asm:alignDraft, pipeline:deNovoPipeline_spoa:medakaConsensus, pipeline:collectFilesInDir, medakaConsensus, sortBam, alignDraft, validate_sample_sheet, alignPolished, pipeline:deNovoPipeline_spoa:spoa, sanitizeRefFile, pipeline:makeReport, trimAndQC, spoa, pipeline:deNovoPipeline_asm:mosdepthPerBase, subsetRefFile, concatTSVs, configure_igv, porechop, mergeVCFs, catFastqIntoFasta, pipeline:getVersions, concatMosdepthResultFiles, pipeline:concatTSVs, split_fq_file, addMedakaToVersionsFile, pipeline:deNovoPipeline_asm:alignPolished, mosdepth, pipeline:porechop, pipeline:deNovoPipeline_asm:medakaConsensus, pipeline:deNovoPipeline_asm:racon, pipeline:deNovoPipeline_spoa:alignPolished, bamstatsDraft, catSortBams, pipeline:deNovoPipeline_asm:bamstatsPolished
Jul-06 06:46:31.093 [main] DEBUG nextflow.Session - Igniting dataflow network (39)
Jul-06 06:46:31.098 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Jul-06 06:46:31.099 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions
Jul-06 06:46:31.099 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:addMedakaToVersionsFile
Jul-06 06:46:31.099 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams
Jul-06 06:46:31.100 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:subsetReads
Jul-06 06:46:31.101 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:porechop
Jul-06 06:46:31.101 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:lookupMedakaModel
Jul-06 06:46:31.103 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:miniasm
Jul-06 06:46:31.104 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:racon
Jul-06 06:46:31.106 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:alignDraft
Jul-06 06:46:31.106 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:medakaConsensus
Jul-06 06:46:31.106 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:bamstatsDraft
Jul-06 06:46:31.107 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:mosdepthPerBase
Jul-06 06:46:31.107 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:trimAndQC
Jul-06 06:46:31.108 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:alignPolished
Jul-06 06:46:31.108 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:bamstatsPolished
Jul-06 06:46:31.110 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_asm:mosdepthWindows
Jul-06 06:46:31.111 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:lookupMedakaModel
Jul-06 06:46:31.112 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:spoa
Jul-06 06:46:31.112 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:alignDraft
Jul-06 06:46:31.112 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:medakaConsensus
Jul-06 06:46:31.113 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:bamstatsDraft
Jul-06 06:46:31.113 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:mosdepthPerBase
Jul-06 06:46:31.113 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:trimAndQC
Jul-06 06:46:31.114 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:alignPolished
Jul-06 06:46:31.114 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:bamstatsPolished
Jul-06 06:46:31.114 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:deNovoPipeline_spoa:mosdepthWindows
Jul-06 06:46:31.115 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:concatTSVs
Jul-06 06:46:31.115 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:catFastqIntoFasta
Jul-06 06:46:31.115 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:collectFilesInDir
Jul-06 06:46:31.116 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeReport
Jul-06 06:46:31.116 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:configure_igv
Jul-06 06:46:31.117 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Jul-06 06:46:31.117 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jul-06 06:46:31.117 [main] DEBUG nextflow.Session - Session await
Jul-06 06:46:31.295 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:31.298 [Task submitter] INFO  nextflow.Session - [a7/be7222] Submitted process > pipeline:getVersions
Jul-06 06:46:31.306 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.312 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.313 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:31.314 [Task submitter] INFO  nextflow.Session - [4b/793ca7] Submitted process > fastcat (1)
Jul-06 06:46:31.317 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.323 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:31.323 [Task submitter] INFO  nextflow.Session - [c7/8891d6] Submitted process > pipeline:getParams
Jul-06 06:46:31.327 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.334 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:31.334 [Task submitter] INFO  nextflow.Session - [76/59957f] Submitted process > fastcat (2)
Jul-06 06:46:31.338 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.346 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:31.347 [Task submitter] INFO  nextflow.Session - [0d/612b46] Submitted process > pipeline:deNovoPipeline_spoa:lookupMedakaModel
Jul-06 06:46:31.351 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.360 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:31.360 [Task submitter] INFO  nextflow.Session - [20/5410fc] Submitted process > pipeline:deNovoPipeline_asm:lookupMedakaModel
Jul-06 06:46:31.364 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.411 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.412 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.414 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.415 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:31.417 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:33.128 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/c7/8891d631767b7d3f2ac25d4976af1f]
Jul-06 06:46:33.152 [Actor Thread 13] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:33.433 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: fastcat (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/4b/793ca75a60c2957a47f34dca842a33]
Jul-06 06:46:33.458 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:33.484 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:33.485 [Task submitter] INFO  nextflow.Session - [27/334c88] Submitted process > pipeline:subsetReads (1)
Jul-06 06:46:33.487 [Actor Thread 18] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:33.535 [Actor Thread 18] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:33.654 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: pipeline:deNovoPipeline_asm:lookupMedakaModel; status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/20/5410fc5283fb850c4114cdf245810c]
Jul-06 06:46:33.664 [Actor Thread 11] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:34.831 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: pipeline:deNovoPipeline_spoa:lookupMedakaModel; status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/0d/612b46a41afd311d9129a32c6b6ac8]
Jul-06 06:46:34.840 [Actor Thread 13] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:35.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: fastcat (2); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/76/59957fe8af72724bb20574db2977d6]
Jul-06 06:46:35.188 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:35.222 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:35.228 [Task submitter] INFO  nextflow.Session - [ac/6d2e26] Submitted process > pipeline:subsetReads (2)
Jul-06 06:46:35.236 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:35.265 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:36.697 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: pipeline:subsetReads (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/27/334c8806ee666b76ce7ecced5a5e0d]
Jul-06 06:46:36.705 [Actor Thread 17] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:36.717 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:36.717 [Task submitter] INFO  nextflow.Session - [1a/3507f9] Submitted process > pipeline:porechop (1)
Jul-06 06:46:36.720 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:36.799 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:37.531 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: pipeline:subsetReads (2); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/ac/6d2e26184f62cbe9d3991a23c97e16]
Jul-06 06:46:37.540 [Actor Thread 13] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:37.548 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:37.549 [Task submitter] INFO  nextflow.Session - [c7/b18feb] Submitted process > pipeline:porechop (2)
Jul-06 06:46:37.551 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:37.632 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:38.923 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: pipeline:porechop (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/1a/3507f96301968ceadef8baaa475634]
Jul-06 06:46:38.932 [Actor Thread 20] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:38.958 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:38.958 [Task submitter] INFO  nextflow.Session - [4e/253c01] Submitted process > pipeline:deNovoPipeline_asm:miniasm (1)
Jul-06 06:46:38.961 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:39.025 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:39.967 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: pipeline:deNovoPipeline_asm:miniasm (1); status: COMPLETED; exit: 0; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/4e/253c01f7f41c961f1bcdc013d39c43]
Jul-06 06:46:39.988 [Actor Thread 11] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:40.016 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-06 06:46:40.016 [Task submitter] INFO  nextflow.Session - [67/12e5b1] Submitted process > pipeline:deNovoPipeline_spoa:spoa (1)
Jul-06 06:46:40.019 [Actor Thread 11] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:40.070 [Actor Thread 11] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:41.573 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: pipeline:deNovoPipeline_spoa:spoa (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/67/12e5b12503e7050f2dd4241eb510d0]
Jul-06 06:46:41.576 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=pipeline:deNovoPipeline_spoa:spoa (1); work-dir=/mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/67/12e5b12503e7050f2dd4241eb510d0
  error [nextflow.exception.ProcessFailedException]: Process `pipeline:deNovoPipeline_spoa:spoa (1)` terminated with an error exit status (1)
Jul-06 06:46:41.586 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:deNovoPipeline_spoa:spoa (1)'

Caused by:
  Process `pipeline:deNovoPipeline_spoa:spoa (1)` terminated with an error exit status (1)

Command executed:

  echo 1  # makes some debugging easier

  workflow-glue run_spoa reads.fastq.gz         --relative-min-coverage 0.15         --max-allowed-read-length 5000         -o asm.fasta

Command exit status:
  1

Command output:
  1

Command error:
  1
  [06:46:40 - workflow_glue] Bootstrapping CLI.
  Cannot import pyabpoa, some features may not be available.
  [06:46:40 - workflow_glue] Starting entrypoint.
  [06:46:40 - workflow_glue.runSPOA   ] Get read orientations...
  Traceback (most recent call last):
    File "/mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/bin/workflow-glue", line 7, in <module>
      cli()
    File "/mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/bin/workflow_glue/__init__.py", line 82, in cli
      args.func(args)
    File "/mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/bin/workflow_glue/run_spoa.py", line 109, in main
      interleaved_reads = interleave_lists(fwd, rev)
    File "/mnt/c/Users/Pete/epi2melabs/workflows/epi2me-labs/wf-amplicon/bin/workflow_glue/run_spoa.py", line 66, in interleave_lists
      rate_2 = 1 / len(l2)
  ZeroDivisionError: division by zero

Work dir:
  /mnt/c/Users/Pete/epi2melabs/instances/wf-amplicon_01J23CP0833A86ZMDDC20972Q9/work/67/12e5b12503e7050f2dd4241eb510d0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Jul-06 06:46:41.590 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `pipeline:deNovoPipeline_spoa:spoa (1)` terminated with an error exit status (1)
Jul-06 06:46:41.592 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:41.606 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] pipeline:addMedakaToVersionsFile
  status=ACTIVE
  port 0: (value) OPEN  ; channel: old_versions.txt
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:miniasm
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:racon
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:alignDraft
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:medakaConsensus
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: medaka_model
  port 2: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:bamstatsDraft
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:mosdepthPerBase
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:trimAndQC
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: asm_method
  port 2: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:alignPolished
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:bamstatsPolished
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_asm:mosdepthWindows
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: n_windows
  port 2: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:spoa
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:alignDraft
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:medakaConsensus
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: medaka_model
  port 2: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:bamstatsDraft
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:mosdepthPerBase
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:trimAndQC
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: asm_method
  port 2: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:alignPolished
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:bamstatsPolished
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:deNovoPipeline_spoa:mosdepthWindows
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: n_windows
  port 2: (cntrl) -     ; channel: $

[process] pipeline:concatTSVs
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: fname
  port 2: (cntrl) -     ; channel: $

[process] pipeline:catFastqIntoFasta
  status=ACTIVE
  port 0: (value) OPEN  ; channel: cons_seqs/seq*.fastq
  port 1: (cntrl) -     ; channel: $

[process] pipeline:collectFilesInDir
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:makeReport
  status=ACTIVE
  port 0: (value) OPEN  ; channel: data/*
  port 1: (value) bound ; channel: ref
  port 2: (value) bound ; channel: sample_sheet
  port 3: (value) OPEN  ; channel: versions.txt
  port 4: (value) bound ; channel: params.json
  port 5: (cntrl) -     ; channel: $

[process] pipeline:configure_igv
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: file-names.txt
  port 1: (queue) OPEN  ; channel: locus_str
  port 2: (value) bound ; channel: bam_extra_opts
  port 3: (queue) OPEN  ; channel: vcf_extra_opts
  port 4: (cntrl) -     ; channel: $

[process] output
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

Jul-06 06:46:41.607 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:41.997 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-06 06:46:41.997 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-06 06:46:42.021 [Actor Thread 25] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-06 06:46:42.155 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (2)
Jul-06 06:46:42.164 [main] DEBUG n.executor.local.LocalTaskHandler - Unable to kill pipeline:getVersions -- command: kill -TERM 8162; exit: 1 
 bash: line 1: kill: (8162) - No such process

Jul-06 06:46:42.168 [Actor Thread 19] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:42.170 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=9; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=2; succeedDuration=9.7s; failedDuration=1.5s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=6; peakCpus=12; peakMemory=12 GB; ]
Jul-06 06:46:42.171 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-06 06:46:42.171 [Actor Thread 14] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:42.173 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-06 06:46:42.199 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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Jul-06 06:46:42.502 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-06 06:46:42.552 [Actor Thread 14] DEBUG nextflow.trace.WebLogObserver - Successfully sent message to http://172.25.192.1:52436 -- received status code 200.
Jul-06 06:46:42.563 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-06 06:46:42.583 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

julibeg commented 4 months ago

Hi @Andreas-Bio!

Thanks for raising this; looks like the error occurs when all reads are in the same direction. The issue should be fixed in the next release. Once it has been published, I will come back to this thread and ask you to confirm that the fix indeed solved your problem. Thanks for your patience!

julibeg commented 4 months ago

Hi @Andreas-Bio, I could reproduce the issue with FASTQ data containing only reads from the same strand. I'm somewhat confused as to how this happened in your case though. Would you mind sharing the raw FASTQ you used when you encountered the error? Thanks!

julibeg commented 3 months ago

Hi @Andreas-Bio, with v1.1.2 the workflow no longer fails if all reads come from the same strand. Please re-open this issue if this does not fix the problem. Thanks!